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Was it one of the Eisenhorn books or was it a Gaunt book?

In the First Eisenhorn Book there is a couple of fights involving a lone member of the Emperors Children legion. Is that what you were thinking of?

Maybe it was Eisenhorn.

Were there any with Gaunt?

there's at least one gaunt book where they generally fight against guard, but then the chaos marine shows up and they pull out the plasma gun/ torrent of fire.

I think in all the Gaunt books they fight multiple chaos marines at a time. Though there is one book (Traitor General I think) where they take out a whole squad of CSM individually.

The Eisenhorn/Mandragore thing was epic. Loved that.

Mandragore...hmm...

The scene I remember is la la la la everything is fine. Oh
crap! A Chaos Marine!

Yeah, that doesn't help much.

I'll have to check my copy of Eisenhorn (I think I lost
the other two books).

Well there is a recent (Michael Harris-like) 40K novel called "Lord of the Night" where a Night Lords Raptor named Sahaal takes on pretty much a whole Imperial world and ultimately wins (and loses at the same time).

You may be thinking of the first book of the series. First and Only, In that one there is a scene where the ghosts take on a Chaos Marine inside a munitions warehouse after he appears out of an elevator.

that sounds like the one I read.

I found it. The first Gaunt book, early pages. Tanith and
Gaunt are attacking a Chaos tainted Forgeworld, and they're
slaughtering the rebels when they face two Iron Warriors.
First one, then the other.